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As I was trying to do some patching on Ubuntu's kernel I've found out kernel.org's patches cannot be merged correctly with the kernel source. I'm wondering if distributions like Ubuntu have their own kernels different from official ones?

Another thing that I think could be related to this question is the name of the directory of source tree in Ubuntu that is linux-headers-2.6.31-21. What does that 21 stand for? Also there is a directory named linux-headers-2.6.31-21-generic. What's the difference between these two?

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Yes, all major distributions customizes their kernel. I use Mandriva Linux and they have some 500 patches to the kernel, but the system works well with the Vanilla (original) kernel, too.

Usually the last number, in your case 21, shows the build number of your customized kernel. In other words, Ubuntu built 21 different kernels from the original sources of 2.6.31 until they reached the current state.

Some directories are also customized to let applications differentiate between several kernels if you have more than one installed.

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